VMD-L Mailing List
From: Peter Mawanga (peter.mawanga.lagos_at_gmail.com)
Date: Thu May 25 2017 - 02:13:12 CDT
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Hello to all
I am trying to remove sudden RMSD jumps between two segments (AP1 and AP2),
observed as an artefact of periodic conditions.
I have tried the commands below (or similar variations), but have not been
able to resolve this:
pbc unwrap -sel "segname AP1 AP2"
pbc wrap -all -sel "segname AP1 AP2" -compound fragment -compoundref
"segname AP1 AP2" -center unitcell -centersel "segname AP1"
I think this should be working as per the PBCTools manual:
http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
Please let me know if there is any error or some omission in the commands.
Feel free to ask for further information.
-- Cheers Peter
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